Hi, I run into problems with StAX when using JSBML (0.8-b2 with dependencies bundled: http://sourceforge.net/projects/jsbml/files/jsbml/0.8-b2/jsbml-0.8-b2-with-dependencies.jar/download ); specifically, SBMLWriter.write method. JSBML depends, among others, on Woodstox StAX implementation (woodstox-core-lgpl-4.0.9.jar). After pruning the problem (see attached workflow) I've reached a point where it turned out that from beanshell in Taverna a "com.sun.xml.internal.stream.XMLOutputFactoryImpl" implementation is used instead of the "javax.xml.stream.XMLOutputFactory" interface, instead of "com.ctc.wstx.stax.WstxOutputFactory". The latter is required as the JSBML code tries to set Woodstox-specific property. I've looked for a way to tell from the running code to use desired implementation. I've only found the following method:
System.setProperty("javax.xml.stream.XMLOutputFactory",
"com.ctc.wstx.stax.WstxOutputFactory");
but this results in
javax.xml.stream.FactoryFinder$ConfigurationError: Provider
com.ctc.wstx.stax.WstxOutputFactory not found
although the class is provided with installed, additional JSBML lib.
Can I force Taverna (Beanshell interpreter?) to use the StAX
implementation provided with Beanshell's JAR dependency? How?
Best regards,
Mikołaj
woodstoxTest.t2flow
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